owltools.panther
Class PANTHERTree

java.lang.Object
  extended by owltools.panther.PANTHERTree

public class PANTHERTree
extends Object

Methods to simplify the work with the Newick-ish output we get from PANTHER.


Constructor Summary
PANTHERTree(File pFile)
          Create an instance for the given path
 
Method Summary
 Set<String> associatedIdentifierSet()
          Return a set of all identifiers associated with this family.
 Set<String> getAncestorAnnotations(String baseGpID)
          Return all annotations to ancestor nodes.
 Set<String> getAncestors(String nodeID)
          Return the ancestors of this node as an ID set.
 Set<String> getDescendantAnnotations(String baseGpID)
          Return all annotations to descendant nodes.
 Set<String> getDescendants(String nodeID)
          Return the descendants of this node as an ID set.
 String getNHXString()
          Return the raw Newick-type input string.
 OWLShuntGraph getOWLShuntGraph()
          Return the complete OWL shunt graph repesentation of the phylogenic tree.
 String getTreeID()
          Return the tree identifier.
 String getTreeLabel()
          Return the tree label.
 String setTreeLabel(String lbl)
          Set the tree label.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

PANTHERTree

public PANTHERTree(File pFile)
            throws IOException
Create an instance for the given path

Parameters:
path -
Throws:
IOException
Method Detail

getNHXString

public String getNHXString()
Return the raw Newick-type input string.


getTreeLabel

public String getTreeLabel()
Return the tree label.


setTreeLabel

public String setTreeLabel(String lbl)
Set the tree label.


getTreeID

public String getTreeID()
Return the tree identifier.


getOWLShuntGraph

public OWLShuntGraph getOWLShuntGraph()
Return the complete OWL shunt graph repesentation of the phylogenic tree.


getAncestors

public Set<String> getAncestors(String nodeID)
Return the ancestors of this node as an ID set. Includes this node. null if nothing is in the graph.

Parameters:
node - id
Returns:
all ancestors (inclusive)

getDescendants

public Set<String> getDescendants(String nodeID)
Return the descendants of this node as an ID set. Includes this node. null if nothing is in the graph.

Parameters:
node - id
Returns:
all ancestors (inclusive)

getAncestorAnnotations

public Set<String> getAncestorAnnotations(String baseGpID)
Return all annotations to ancestor nodes.

Parameters:
gene - product id
Returns:
all ancestor annotations (inclusive)

getDescendantAnnotations

public Set<String> getDescendantAnnotations(String baseGpID)
Return all annotations to descendant nodes.

Parameters:
gene - product id
Returns:
all descendant annotations (inclusive)

associatedIdentifierSet

public Set<String> associatedIdentifierSet()
Return a set of all identifiers associated with this family.



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